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Receptor
PDB id Resolution Class Description Source Keywords
1U08 2.35 Å EC: 2.6.1.- CRYSTAL STRUCTURE AND REACTIVITY OF YBDL FROM ESCHERICHIA CO IDENTIFY A METHIONINE AMINOTRANSFERASE FUNCTION. ESCHERICHIA COLI ALPHA BETA PROTEIN TRANSFERASE
Ref.: CRYSTAL STRUCTURE AND REACTIVITY OF YBDL FROM ESCHE COLI IDENTIFY A METHIONINE AMINOTRANSFERASE FUNCTIO FEBS LETT. V. 571 141 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLP A:400;
B:1400;
Valid;
Valid;
none;
none;
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247.142 C8 H10 N O6 P Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1U08 2.35 Å EC: 2.6.1.- CRYSTAL STRUCTURE AND REACTIVITY OF YBDL FROM ESCHERICHIA CO IDENTIFY A METHIONINE AMINOTRANSFERASE FUNCTION. ESCHERICHIA COLI ALPHA BETA PROTEIN TRANSFERASE
Ref.: CRYSTAL STRUCTURE AND REACTIVITY OF YBDL FROM ESCHE COLI IDENTIFY A METHIONINE AMINOTRANSFERASE FUNCTIO FEBS LETT. V. 571 141 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1U08 - PLP C8 H10 N O6 P Cc1c(c(c(c....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1U08 - PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1GDE - GLU PLP n/a n/a
2 1V2F - HCI C9 H10 O2 c1ccc(cc1)....
3 1U08 - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 1GCK - ASP PLP n/a n/a
5 1XI9 - PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLP; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 1 1
2 PZP 0.729167 0.843137
3 EXT 0.62069 0.8
4 AN7 0.603448 0.918367
5 EPC 0.603448 0.862745
6 FOO 0.59322 0.849057
7 PLR 0.58 0.895833
8 4LM 0.57377 0.818182
9 0JO 0.57377 0.803571
10 P3D 0.571429 0.704918
11 F0G 0.564516 0.865385
12 MPM 0.564516 0.814815
13 FEV 0.555556 0.803571
14 KOU 0.555556 0.836364
15 HCP 0.546875 0.77193
16 EVM 0.546875 0.821429
17 6DF 0.545455 0.811321
18 PXL 0.541667 0.659574
19 Z98 0.537313 0.75
20 PXP 0.537037 0.862745
21 PMP 0.527273 0.767857
22 P0P 0.527273 0.916667
23 PL6 0.522388 0.818182
24 GT1 0.517857 0.830189
25 PFM 0.514706 0.803571
26 FEJ 0.514706 0.851852
27 LLP 0.5 0.737705
28 P70 0.5 0.833333
29 PUS 0.479452 0.707692
30 PL5 0.479452 0.775862
31 MPL 0.473684 0.836364
32 PLG 0.46875 0.75
33 IN5 0.46875 0.758621
34 P89 0.466667 0.714286
35 PLP PUT 0.463768 0.672131
36 EQJ 0.460526 0.725806
37 5DK 0.460526 0.725806
38 O1G 0.454545 0.75
39 PLT 0.439024 0.762712
40 X04 0.431034 0.851852
41 PDD 0.426471 0.762712
42 PP3 0.426471 0.762712
43 PDA 0.426471 0.762712
44 P1T 0.426471 0.714286
45 33P 0.42029 0.745763
46 IK2 0.42029 0.714286
47 TLP 0.414286 0.793103
48 2BK 0.414286 0.793103
49 PLS 0.414286 0.779661
50 2BO 0.414286 0.793103
51 5PA 0.414286 0.714286
52 PMH 0.414286 0.619718
53 9TD 0.413793 0.671642
54 PLP 999 0.410959 0.796296
55 PPD 0.408451 0.75
56 C6P 0.408451 0.75
57 QLP 0.405405 0.681818
58 MP5 0.403509 0.666667
59 PLA 0.402778 0.703125
60 PY5 0.402778 0.703125
61 HEY 0.4 0.703125
62 PLP PHE 0.4 0.732143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1U08; Ligand: PLP; Similar sites found with APoc: 167
This union binding pocket(no: 1) in the query (biounit: 1u08.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3ZL8 ADP 1.29534
2 5K8B PDG 1.29534
3 4TQK NAG 1.29534
4 5GSN MMZ 1.5544
5 2WQN ADP 1.6129
6 1MLY ACZ PLP 1.81347
7 1VJ7 GDP 1.81347
8 2ZRU FMN 1.90217
9 3WGC PLG 2.05279
10 6C3C EJ1 2.07254
11 5GVL PLG 2.07254
12 5GVL GI8 2.07254
13 1CL2 PPG 2.07254
14 4ZSY RW2 2.07254
15 3BEO UDP 2.13333
16 6ECG PM9 2.33161
17 2TPL HPP 2.33161
18 1PMO PLR 2.33161
19 4LNL PLG 2.4024
20 4LNL 2BO 2.4024
21 4LNL 2BK 2.4024
22 2Z9V PXM 2.59067
23 2FYF PLP 2.59067
24 6FYQ PLP 2.59067
25 1SFF IK2 2.59067
26 5DDW 5B6 2.59067
27 5ENZ UDP 2.5974
28 1O69 X04 2.84974
29 3FQ8 PMP 2.84974
30 4B98 PXG 2.84974
31 2G50 PYR 2.84974
32 5CAD PCA 2.84974
33 1LW4 PLP 2.88184
34 1LW4 TLP 2.88184
35 3ITJ CIT 2.95858
36 6CZY PMP 3.03867
37 1JS3 PLP 142 3.08642
38 3BWN PMP 3.10881
39 3BWN PMP PHE 3.10881
40 4E1O PLP PVH 3.10881
41 3VP6 HLD 3.13112
42 3RI1 3RH 3.19489
43 2OGA PGU 3.36788
44 1VGV UD1 3.38542
45 4NES UDP 3.47594
46 2YIP YIO 3.62319
47 4WXG 2BO 3.62694
48 1FC4 AKB PLP 3.62694
49 5W70 9YM 3.62694
50 1K4M CIT 3.75587
51 4ADC PLP 3.88601
52 4IP7 FLC 3.88601
53 4OKS 2T9 3.88601
54 5J60 FAD 4.0625
55 4EXO PYR 4.10959
56 4WZ6 ATP 4.13793
57 5IWQ PLP 4.14508
58 2WK9 PLP 4.14508
59 2WK9 PLG 4.14508
60 6CD1 PLS 4.14508
61 5WYF ILP 4.14508
62 3VSS FRU 4.14508
63 1VJO PLP 4.14508
64 6CD1 PLG 4.14508
65 2HOX P1T 4.40415
66 4E3Q PMP 4.40415
67 5G4J EXT 4.40415
68 3HQP OXL 4.40415
69 1T0S BML 4.65116
70 4UHO PLP 4.66321
71 2C1X UDP 4.66321
72 1B9I PXG 4.66321
73 3ZRR PXG 4.6875
74 4HVK PMP 4.71204
75 5JQ1 ZPF 4.82759
76 5KGS 6SR 4.92228
77 5W19 9TD 4.92228
78 1F6D UDP 5.05319
79 5TXR PLP 5.18135
80 3PFD FDA 5.18135
81 4ZM4 P3B 5.18135
82 4ZM4 PLP 5.18135
83 5DT6 GLU 5.24345
84 4DW4 U5P 5.38922
85 1ZC9 PMP 5.44041
86 3BS8 PMP 5.44041
87 2AY3 MPP 5.44041
88 6CBO DOW 5.69948
89 1WYV PLP AOA 5.95855
90 5U23 TQP 6.02094
91 4OKD GLC GLC GLC 6.21762
92 4AT0 FAD 6.21762
93 4WQQ MAN 6.38298
94 1KJ1 MAN 6.42202
95 3PNL ADP 6.63507
96 4BA5 PXG 6.73575
97 3P7N FMN 6.97674
98 2FNU PMP UD1 7.2
99 5OMY 9YE 7.25389
100 4UOX PLP 7.51295
101 1DJ9 KAM 7.55208
102 4RJD TFP 7.57576
103 3IHB GLU 7.77202
104 4WXJ GLU 7.80669
105 5WS9 OXL 8.03109
106 5WS9 ATP 8.03109
107 2PZE ATP 8.29694
108 3A8U PLP 8.80829
109 4AZJ SEP PLP 8.88889
110 2PO3 T4K 9.06736
111 5M3Z PLP 9.58549
112 5M3Z PY6 9.58549
113 5M3Z NLE 9.58549
114 3FRK TQP 10.1877
115 4RKC PMP 10.3627
116 1DFO PLG 10.3627
117 2CJH AKG 10.6218
118 5ODQ FAD 10.7143
119 3CR3 ADP 10.7438
120 1E5F PLP 10.8911
121 4IY7 KOU 11.1399
122 4IYO 0JO 11.1399
123 4IY7 0JO 11.1399
124 1OXO IK2 11.399
125 2XBN PMP 11.399
126 2Q4W FAD 11.399
127 5X30 7XF 12.1762
128 5X30 4LM 12.1762
129 1TOI HCI 12.1762
130 5X2Z 3LM 12.1762
131 3RYC GDP 12.1762
132 5EIB GTP 12.1762
133 6DND PLP 12.6943
134 4K2M O1G 12.9534
135 1AJS PLA 13.2124
136 4AOA IK2 13.2124
137 5YKT PMP 13.4715
138 3DR4 G4M 13.4715
139 3B8X G4M 13.4715
140 3NUB UD0 13.9276
141 2X5F PLP 15.0259
142 1ELU PDA 15.285
143 1ELU CSS 15.285
144 1MDZ PLP 19.9482
145 1MDZ DCS 19.9482
146 6EWR PMP 20.4663
147 1C7O PPG 20.7254
148 1LC8 33P 22.5275
149 4JE5 PMP 22.5389
150 4JE5 PLP 22.5389
151 3CQ5 PMP 23.3062
152 3PD6 PMP 24.6114
153 3PDB PMP 24.6114
154 1UU1 PMP HSA 28.6567
155 4ZAH T5K 29.2929
156 6C9B EGV 30.5851
157 6C92 EQJ 30.8511
158 6C8T EQJ 30.8511
159 4M2K PLP 33.6788
160 1GEX PLP HSA 34.2697
161 2ZYJ PGU 35.7513
162 3EI9 PL6 36.0104
163 2R2N PMP 36.5285
164 2R2N KYN 36.5285
165 1M7Y PPG 36.7876
166 2ZC0 PMP 39.8964
167 2X5D PLP 41.1917
Pocket No.: 2; Query (leader) PDB : 1U08; Ligand: PLP; Similar sites found with APoc: 13
This union binding pocket(no: 2) in the query (biounit: 1u08.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4GXQ ATP 1.29534
2 5YLT C7N 2.28137
3 5YLT SFG 2.28137
4 4IVN BMX 3.23741
5 5UAO FAD 3.32717
6 1Z0S ATP 3.59712
7 2WPB ZZI 4.14508
8 3ZQE DXC 4.91803
9 5TA6 79D 5.69948
10 4POJ 2VP 6.92641
11 4UOX PUT 7.51295
12 1GTE IUR 8.54922
13 1GTE FMN 8.54922
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